ArticleNucleic acids research2024
Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry.The New phytologist · 2026Article
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
- Epigenetic changes and heat stress activate Helitron mobility in wheat.Nature plants · 2026Article
- An active Helitron transposon family in wheat.Nature plants · 2026Article
- Reproductive mode and ploidy are associated with distinct organization of clustered centromeric regions in Meloidogyne nematodes.Genome biology · 2026Article
- Regions of low gene expression promote maintenance and adaptation of horizontally acquired genes in yeasts.Communications biology · 2026Article
- Genome reshaping by Helitron transposons in Fusarium oxysporum TR4 affects secondary metabolism but not virulence.Nature communications · 2026Article
- The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.BMC biology · 2026Article
- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- De Novo Chromosome-Level Assembly of the Endangered Pilocarpus Microphyllus Highlights Genomic Resources for Conservation and Sustainable Pilocarpine Extraction.Genome biology and evolution · 2026Article
- Chromosome-level genome assembly of the AustralianFrontiers in plant science · 2026Article
- Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).Genome biology and evolution · 2025Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- Impact of a horizontally transferred Helitron family on genome evolution in Xenopus laevis.Mobile DNA · 2025Article
- Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
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4 authors.
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Abstract
Helitron-like elements (HLEs) are widespread eukaryotic DNA transposons employing a rolling-circle transposition mechanism. Despite their prevalence in fungi, animals, and plant genomes, identifying Helitrons remains a formidable challenge. We introduce HELIANO, a software for annotating and classifying autonomous and non-autonomous HLE sequences from whole genomes. HELIANO overcomes several limitations of existing tools in speed and accuracy, demonstrated through benchmarking and its application to the complex genomes of frogs (Xenopus tropicalis and Xenopus laevis) and rice (Oryza sativa), where it uncovered numerous previously unidentified HLEs. In an extensive analysis of 404 eukaryote genomes, we found HLEs widely distributed across phyla, with exceptions in specific taxa. HELIANO's application led to the discovery of numerous new HLEs in land plants and identified 20 protein domains captured by certain autonomous HLE families. A comprehensive phylogenetic analysis further classified HLEs into two primary clades, HLE1 and HLE2, and revealed nine subgroups, some of which are enriched within specific taxa. The future use of HELIANO promises to improve the global analysis of HLEs across genomes, significantly advancing our understanding of this fascinating transposon superfamily.
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